I've been looking for water quality information on such pools, and finally found some:

Natural Swimming Pools in Lower Saxony
Ernst-August Heinemeyer, Health Authority of Lower Saxony, Aurich, Germany

Experience with a „natural tropic pool”
Christiane Höller and Schindler P., Bavarian Health and Food Safety Authority, Germany

A Model for Risk Assessment for Small-scale Bathing Ponds
Franz Mascher1, Pichler-Semmelrock P.2, Reinthaler F.1, and Marth E.1, 1Institute of Hygiene, Medical-University, Graz; 2Federal Government of Steiermark, Austria

A quote from the first article is sufficient to show that such pools are not 'home-free' when it comes to sanitation:
Amounts of P. aeruginosa exceeding the limits were detected in almost every natural swimming pool, in some pools on a regular basis
All articles have been archived at Swimming Pool Research, so if the links die, I can restore them.